Research workbench
Crystal structure of anti-zika antibody Z021 bound to denv-1 envelope protein diii
Analyse Crystal structure of anti-zika antibody Z021 bound to denv-1 envelope protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DFJ
- Type
- protein
- Length
- 532 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-zika antibody Z021, heavy chain; Anti-zika antibody Z021, light chain; Dengue 1…
- UniProt
- Q8BE58
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-zika antibody Z021, heavy chain | protein | 219 | 7% helix, 53% strand | — |
| L | Anti-zika antibody Z021, light chain | protein | 214 | 6% helix, 51% strand | — |
| E | Dengue 1 envelope diii domain | protein | 99 | 3% helix, 45% strand | Q8BE58 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.63 | 0.74 | 64 | empty |
| 2 | 51 | 0.53 | 0.89 | 18 | empty |
| 3 | 155 | 0.47 | 0.76 | 22 | empty |
| 4 | 107 | 0.36 | 0.74 | 21 | empty |
| 5 | 69 | 0.28 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2036 Ų buried · 20 hydrogen bonds · protein-protein
- H–E · 537 Ų buried · 9 hydrogen bonds · protein-protein
- L–E · 336 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6DFJ · Crystal structure of anti-Zika antibody Z021 bound to DENV-1 envelope protein DIII · the same entry in another collection · chain H against H, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8BE58
- Elsewhere: RCSB PDB 6DFJ · PDBe 6DFJ · UniProt Q8BE58
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